Figure 3: Representation of potential bi-directional signalling pathway.

(a) Model of the upper α-ring and the adjacent regions of Rpn5 and Rpn6 are shown coloured according to their B-factors. For better orientation, the HbYX motifes of Rpt3 and Rpt5 are depicted in their binding pockets (green and cyan) and the orange arch corresponds to the position of Rpt3’s region with highest B-factors. A significant increase in B-factors can be seen on the outer parts of α2, α3 and α 4 which all are adjacent to the Oprozomib binding subunit β5. The regulatory subunits Rpn5 and Rpn6, which directly bind the α-ring, show the highest B-factors, presenting a potential communication path indicated by flexible parts. (b) The model of the ATPase ring and the adjacent parts of Rpn5 and 6 are shown coloured by B-factors. The perspective onto the segment is the same as in a. A similar distribution of B-Factors as in a can be seen. Subunits Rpt2, 6 and 3 show increased B-factors as they are adjacent to the more mobile α-subunits in a. Similarly, the regulatory subunits Rpn5 and 6 show very high B-factors. Right: to analyse the symmetry of the ATPase, three conserved amino acids have been chosen in all six. The Cα-atoms have been connected and the inner angles of the resulting hexagons enclosed by Rpt6, Rpt2 and Rpt1 have been calculated. Whereas the C-terminal region of the ATPase forms a perfectly regular hexagon, the symmetry is clearly broken in the N-terminal region near the centre of the ATPase. This deviation from perfect symmetry indicates the required motion for ATPase activity and is consistent with an increase in model B factors. (c) Focused classification on the Rpn9/10 (orange) region and subsequent refinement in RELION revealed different conformational states for the receptor regions. Only exemplary conformations are shown. Similar conformations can be found by focusing on Rpn5 (blue) only.